diff --git a/cdm-test/src/test/java/ucar/nc2/grib/TestGribIndexLocationS3.java b/cdm-test/src/test/java/ucar/nc2/grib/TestGribIndexLocationS3.java
index 9eef8a1fcb..a312568f46 100644
--- a/cdm-test/src/test/java/ucar/nc2/grib/TestGribIndexLocationS3.java
+++ b/cdm-test/src/test/java/ucar/nc2/grib/TestGribIndexLocationS3.java
@@ -1,3 +1,8 @@
+/*
+ * Copyright (c) 2023-2026 University Corporation for Atmospheric Research/Unidata
+ * See LICENSE for license information.
+ */
+
 package ucar.nc2.grib;
 
 import static com.google.common.truth.Truth.assertThat;
@@ -51,7 +56,7 @@ public static List<Object[]> getTestParameters() {
 
   public TestGribIndexLocationS3(String filename, String fragment) {
     this.filename = filename + fragment;
-    this.indexFilename = filename + GribIndex.GBX9_IDX;
+    this.indexFilename = GribIndex.makeIndexFileName(filename);
     this.isGrib1 = filename.endsWith(".grib1");
   }
 
@@ -86,7 +91,7 @@ public void shouldCreateIndexInDefaultCache() throws IOException {
     assertThat(index).isNotNull();
     assertThat(index.getNRecords()).isNotEqualTo(0);
 
-    assertThat(diskCache.getCacheFile(s3File.getPath() + GribIndex.GBX9_IDX).exists()).isTrue();
+    assertThat(diskCache.getCacheFile(GribIndex.makeIndexFileName(s3File.getPath())).exists()).isTrue();
   }
 
   @Test
@@ -98,13 +103,13 @@ public void shouldReuseCachedIndex() throws IOException {
     final GribIndex index =
         GribIndex.readOrCreateIndexFromSingleFile(isGrib1, s3File, CollectionUpdateType.always, logger);
     assertThat(index).isNotNull();
-    assertThat(diskCache.getCacheFile(s3File.getPath() + GribIndex.GBX9_IDX).exists()).isTrue();
-    final long cacheLastModified = diskCache.getCacheFile(s3File.getPath() + GribIndex.GBX9_IDX).lastModified();
+    assertThat(diskCache.getCacheFile(GribIndex.makeIndexFileName(s3File.getPath())).exists()).isTrue();
+    final long cacheLastModified = diskCache.getCacheFile(GribIndex.makeIndexFileName(s3File.getPath())).lastModified();
 
     final GribIndex rereadIndex =
         GribIndex.readOrCreateIndexFromSingleFile(isGrib1, s3File, CollectionUpdateType.never, logger);
     assertThat(rereadIndex).isNotNull();
-    final File rereadCachedIndex = diskCache.getCacheFile(s3File.getPath() + GribIndex.GBX9_IDX);
+    final File rereadCachedIndex = diskCache.getCacheFile(GribIndex.makeIndexFileName(s3File.getPath()));
     assertThat(rereadCachedIndex.lastModified()).isEqualTo(cacheLastModified);
   }
 }
diff --git a/cdm/core/src/main/java/thredds/filesystem/ControllerOS.java b/cdm/core/src/main/java/thredds/filesystem/ControllerOS.java
index 1aaa024377..6c401084ff 100644
--- a/cdm/core/src/main/java/thredds/filesystem/ControllerOS.java
+++ b/cdm/core/src/main/java/thredds/filesystem/ControllerOS.java
@@ -78,6 +78,20 @@ public DirectoryStream<MFile> getSubdirs(CollectionConfig mc, boolean recheck) {
     return new MFileDirectoryStream(new FilteredIterator(mc, new MFileIterator(cd), true)); // return only subdirs
   }
 
+  @Nullable
+  @Override
+  public DirectoryStream<MFile> getFullInventoryAtLocation(String location) {
+    if (location.startsWith("file:")) {
+      location = location.substring(5);
+    }
+
+    File cd = new File(location);
+    if (!cd.exists())
+      return null;
+    if (!cd.isDirectory())
+      return null;
+    return new MFileDirectoryStream(new MFileIterator(cd));
+  }
 
   public void close() {} // NOOP
 
diff --git a/cdm/core/src/main/java/thredds/filesystem/ControllerOS7.java b/cdm/core/src/main/java/thredds/filesystem/ControllerOS7.java
index 82543e04d1..61352bcd9d 100644
--- a/cdm/core/src/main/java/thredds/filesystem/ControllerOS7.java
+++ b/cdm/core/src/main/java/thredds/filesystem/ControllerOS7.java
@@ -5,6 +5,7 @@
 
 package thredds.filesystem;
 
+import javax.annotation.Nullable;
 import thredds.inventory.CollectionConfig;
 import thredds.inventory.MController;
 import thredds.inventory.MFile;
@@ -57,6 +58,27 @@ public DirectoryStream<MFile> getSubdirs(CollectionConfig mc, boolean recheck) {
     return null;
   }
 
+  @Nullable
+  @Override
+  public DirectoryStream<MFile> getFullInventoryAtLocation(String location) {
+    if (location.startsWith("file:")) {
+      location = location.substring(5);
+    }
+
+    Path cd = Paths.get(location);
+    if (!Files.exists(cd))
+      return null;
+    if (!Files.isDirectory(cd))
+      return null;
+
+    MFileDirectoryStream stream = null;
+    try {
+      stream = new MFileDirectoryStream(new MFileIterator(cd, null));
+    } catch (IOException ioe) {
+      logger.warn(ioe.getMessage(), ioe);
+    }
+    return stream;
+  }
 
   public void close() {} // NOOP
 
diff --git a/cdm/core/src/main/java/thredds/inventory/CollectionAbstract.java b/cdm/core/src/main/java/thredds/inventory/CollectionAbstract.java
index a21fca8bfe..304e710192 100644
--- a/cdm/core/src/main/java/thredds/inventory/CollectionAbstract.java
+++ b/cdm/core/src/main/java/thredds/inventory/CollectionAbstract.java
@@ -121,7 +121,11 @@ public String getCollectionName() {
 
   @Override
   public String getIndexFilename(String suffix) {
-    return getRoot() + "/" + collectionName + suffix;
+    MFile rootMFile = MFiles.create(getRoot());
+    MFile mfile = rootMFile.getChild(collectionName + suffix);
+    if (mfile == null)
+      throw new IllegalStateException("Cannot determine location of collection index file");
+    return mfile.getPath();
   }
 
   public void setStreamFilter(MFileFilter filter) {
diff --git a/cdm/core/src/main/java/thredds/inventory/CollectionList.java b/cdm/core/src/main/java/thredds/inventory/CollectionList.java
index a895dacc12..5690ff7f2f 100644
--- a/cdm/core/src/main/java/thredds/inventory/CollectionList.java
+++ b/cdm/core/src/main/java/thredds/inventory/CollectionList.java
@@ -42,7 +42,6 @@ public CollectionList(String collectionName, String list, Logger logger) {
 
     Collections.sort(mfiles);
     this.lastModified = lastModified;
-    this.root = System.getProperty("user.dir");
   }
 
   public CollectionList(String collectionName, String root, List<MFile> mfiles, Logger logger) {
diff --git a/cdm/core/src/main/java/thredds/inventory/CollectionManagerCatalog.java b/cdm/core/src/main/java/thredds/inventory/CollectionManagerCatalog.java
index 6e157f9d19..07c9090141 100644
--- a/cdm/core/src/main/java/thredds/inventory/CollectionManagerCatalog.java
+++ b/cdm/core/src/main/java/thredds/inventory/CollectionManagerCatalog.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 1998-2018 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -18,6 +18,7 @@
 import java.util.Date;
 import java.util.Formatter;
 import java.util.List;
+import ucar.nc2.util.DiskCache2;
 
 /**
  * CollectionManager of datasets from a catalog.
@@ -45,7 +46,7 @@ public CollectionManagerCatalog(String collectionName, String collectionSpec, St
     }
 
     this.catalogUrl = collectionSpec;
-    this.root = System.getProperty("user.dir");
+    this.root = DiskCache2.getDefault().getRootDirectory();
   }
 
   @Override
diff --git a/cdm/core/src/main/java/thredds/inventory/CollectionSingleFile.java b/cdm/core/src/main/java/thredds/inventory/CollectionSingleFile.java
index faa81b9d6f..0be93a70ea 100644
--- a/cdm/core/src/main/java/thredds/inventory/CollectionSingleFile.java
+++ b/cdm/core/src/main/java/thredds/inventory/CollectionSingleFile.java
@@ -5,6 +5,8 @@
 
 package thredds.inventory;
 
+import ucar.nc2.util.DiskCache2;
+
 /**
  * A CollectionManager consisting of a single file
  *
@@ -18,9 +20,9 @@ public CollectionSingleFile(MFile file, org.slf4j.Logger logger) {
     mfiles.add(file);
     try {
       MFile p = file.getParent();
-      this.root = p != null ? p.getPath() : System.getProperty("user.dir");
+      this.root = p != null ? p.getPath() : DiskCache2.getDefault().getRootDirectory();
     } catch (java.io.IOException e) {
-      this.root = System.getProperty("user.dir");
+      this.root = DiskCache2.getDefault().getRootDirectory();
     }
 
     this.lastModified = file.getLastModified();
diff --git a/cdm/core/src/main/java/thredds/inventory/CollectionSpecParser.java b/cdm/core/src/main/java/thredds/inventory/CollectionSpecParser.java
index d35d33cc94..f91db7d915 100644
--- a/cdm/core/src/main/java/thredds/inventory/CollectionSpecParser.java
+++ b/cdm/core/src/main/java/thredds/inventory/CollectionSpecParser.java
@@ -1,11 +1,13 @@
 /*
- * Copyright (c) 1998-2022 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
+
 package thredds.inventory;
 
 import java.io.File;
 import java.util.Formatter;
+import ucar.nc2.util.DiskCache2;
 
 /**
  * Parses the collection specification string for local files.
@@ -39,7 +41,7 @@
 public class CollectionSpecParser extends CollectionSpecParserAbstract {
   private final static String DELIMITER = "/";
   private final static String FRAGMENT = "";
-  private final static String DEFAULT_DIR = System.getProperty("user.dir");
+  private final static String DEFAULT_DIR = DiskCache2.getDefault().getRootDirectory();
 
   /**
    * Single spec : "/topdir/** /#dateFormatMark#regExp"
diff --git a/cdm/core/src/main/java/thredds/inventory/MController.java b/cdm/core/src/main/java/thredds/inventory/MController.java
index 1e42dd0f23..e47d206f2f 100644
--- a/cdm/core/src/main/java/thredds/inventory/MController.java
+++ b/cdm/core/src/main/java/thredds/inventory/MController.java
@@ -48,15 +48,13 @@ public interface MController extends Closeable {
   DirectoryStream<MFile> getSubdirs(CollectionConfig mc, boolean recheck);
 
   /**
-   * Get an MFile for a specific location.
-   * 
-   * @param location the location
-   * @return MFile or null
+   * Returns all subdirectories and leaves in a given location, not recursing into subdirectories.
+   *
+   * @param location defines the location to scan
+   * @return DirectoryStream over Mfiles, or null if the location does not exist
    */
   @Nullable
-  default MFile getMFile(String location) {
-    return MFiles.create(location);
-  }
+  DirectoryStream<MFile> getFullInventoryAtLocation(String location);
 
   @Override
   void close();
diff --git a/cdm/core/src/main/java/thredds/inventory/MControllers.java b/cdm/core/src/main/java/thredds/inventory/MControllers.java
index 6a703b4599..1dfbe54784 100644
--- a/cdm/core/src/main/java/thredds/inventory/MControllers.java
+++ b/cdm/core/src/main/java/thredds/inventory/MControllers.java
@@ -43,8 +43,7 @@ public static MController create(String location) {
    */
   public static DirectoryStream<MFile> newDirectoryStream(String location) throws IOException {
     MController controller = create(location);
-    CollectionConfig config = new CollectionConfig(location, location, false, null, null);
-    DirectoryStream<MFile> stream = controller.getInventoryTop(config, true);
+    DirectoryStream<MFile> stream = controller.getFullInventoryAtLocation(location);
     controller.close();
     if (stream == null) {
       throw new IOException("Could not create DirectoryStream for " + location);
diff --git a/cdm/core/src/main/java/thredds/inventory/partition/DirectoryBuilder.java b/cdm/core/src/main/java/thredds/inventory/partition/DirectoryBuilder.java
index 3e8ad497da..154d6ba760 100644
--- a/cdm/core/src/main/java/thredds/inventory/partition/DirectoryBuilder.java
+++ b/cdm/core/src/main/java/thredds/inventory/partition/DirectoryBuilder.java
@@ -71,7 +71,7 @@ private enum PartitionStatus {
   private PartitionStatus partitionStatus = PartitionStatus.unknown;
 
   public DirectoryBuilder(String topCollectionName, String dirFilename, String suffix) throws IOException {
-    this(topCollectionName, MControllers.create(dirFilename).getMFile(dirFilename), suffix);
+    this(topCollectionName, MFiles.create(dirFilename), suffix);
   }
 
   /**
diff --git a/cdm/core/src/test/data/directory_stream/sub_directory/sub_directory_2/subdir2_file b/cdm/core/src/test/data/directory_stream/sub_directory/sub_directory_2/subdir2_file
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/cdm/core/src/test/data/directory_stream/sub_directory/subdir_file b/cdm/core/src/test/data/directory_stream/sub_directory/subdir_file
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/cdm/core/src/test/data/directory_stream/top_level_file b/cdm/core/src/test/data/directory_stream/top_level_file
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/cdm/core/src/test/java/thredds/inventory/TestCollectionSpecParser.java b/cdm/core/src/test/java/thredds/inventory/TestCollectionSpecParser.java
index 35e5bc9ec9..3e4bc4ff64 100644
--- a/cdm/core/src/test/java/thredds/inventory/TestCollectionSpecParser.java
+++ b/cdm/core/src/test/java/thredds/inventory/TestCollectionSpecParser.java
@@ -1,3 +1,8 @@
+/*
+ * Copyright (c) 2019-2026 University Corporation for Atmospheric Research/Unidata
+ * See LICENSE for license information.
+ */
+
 package thredds.inventory;
 
 import static com.google.common.truth.Truth.assertThat;
@@ -12,6 +17,7 @@
 import org.junit.runners.Parameterized;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import ucar.nc2.util.DiskCache2;
 
 @RunWith(Parameterized.class)
 public class TestCollectionSpecParser {
@@ -67,11 +73,11 @@ public static List<Object[]> getTestParameters() throws URISyntaxException {
         {"/data/ldm/pub/decoded/netcdf/surface/metar/T*.T", "/data/ldm/pub/decoded/netcdf/surface/metar", false, "T*.T",
             null},
 
-        {"", System.getProperty("user.dir"), false, null, null},
+        {"", DiskCache2.getDefault().getRootDirectory(), false, null, null},
 
-        {".*grib1", System.getProperty("user.dir"), false, ".*grib1", null},
+        {".*grib1", DiskCache2.getDefault().getRootDirectory(), false, ".*grib1", null},
 
-        {".*\\.grib1", System.getProperty("user.dir"), false, ".*\\.grib1", null},
+        {".*\\.grib1", DiskCache2.getDefault().getRootDirectory(), false, ".*\\.grib1", null},
 
         {"dir/**/subdir/.*grib1", "dir", true, "subdir/.*grib1", null},});
   }
diff --git a/cdm/core/src/test/java/thredds/inventory/TestMControllers.java b/cdm/core/src/test/java/thredds/inventory/TestMControllers.java
new file mode 100644
index 0000000000..aa0613afc7
--- /dev/null
+++ b/cdm/core/src/test/java/thredds/inventory/TestMControllers.java
@@ -0,0 +1,52 @@
+package thredds.inventory;
+
+import static com.google.common.truth.Truth.assertThat;
+
+import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import org.junit.Test;
+import ucar.unidata.util.test.TestDir;
+
+public class TestMControllers {
+
+  @Test
+  public void testDirectoryStream() throws IOException {
+    String testDir = TestDir.localTestDataDir + "directory_stream";
+
+    ArrayList<String> dsMfiles = new ArrayList<>();
+    DirectoryStream<MFile> ds = MControllers.newDirectoryStream(testDir);
+    for (MFile item : ds) {
+      dsMfiles.add(Paths.get(item.getPath()).toAbsolutePath().toString());
+    }
+    ds.close();
+
+    ArrayList<String> dsFiles = new ArrayList<>();
+    DirectoryStream<Path> ds2 =
+        Files.newDirectoryStream(Paths.get(TestDir.localTestDataDir + "directory_stream").toAbsolutePath());
+    for (Path item : ds2) {
+      dsFiles.add(item.toString());
+    }
+    ds2.close();
+
+    dsMfiles.sort(null);
+    dsFiles.sort(null);
+    assertThat(dsMfiles).containsExactlyElementsIn(dsFiles);
+  }
+
+  @Test
+  public void testSubdirStream() throws IOException {
+    String testDir = TestDir.localTestDataDir + "directory_stream";
+    ArrayList<String> dsMfiles = new ArrayList<>();
+    DirectoryStream<MFile> ds = MControllers.newSubdirStream(testDir);
+    for (MFile item : ds) {
+      dsMfiles.add(Paths.get(item.getPath()).toAbsolutePath().toString());
+    }
+    ds.close();
+
+    assertThat(dsMfiles).hasSize(1);
+  }
+}
diff --git a/cdm/s3/src/main/java/thredds/filesystem/s3/ControllerS3.java b/cdm/s3/src/main/java/thredds/filesystem/s3/ControllerS3.java
index 0af11b58a5..6cdf4ace41 100644
--- a/cdm/s3/src/main/java/thredds/filesystem/s3/ControllerS3.java
+++ b/cdm/s3/src/main/java/thredds/filesystem/s3/ControllerS3.java
@@ -51,11 +51,17 @@ public ControllerS3() {}
 
   private void init(CollectionConfig mc) {
     if (mc != null) {
+      init(mc.getDirectoryName());
+    }
+  }
+
+  private void init(String location) {
+    if (location != null) {
       try {
-        initUri(mc.getDirectoryName());
+        initUri(location);
         initClient();
       } catch (IOException e) {
-        logger.error("Error initializing ControllerS3 for {}.", mc.getDirectoryName(), e);
+        logger.error("Error initializing ControllerS3 for {}.", location, e);
       }
     }
   }
@@ -128,6 +134,16 @@ public DirectoryStream<MFile> getSubdirs(CollectionConfig mc, boolean recheck) {
     return new MFileDirectoryStream(new FilteredIterator(mc, mFiles.iterator(), true));
   }
 
+  @Override
+  public DirectoryStream<MFile> getFullInventoryAtLocation(String location) {
+    init(location);
+    String prefix = null;
+    if (initialUri.getKey().isPresent()) {
+      prefix = initialUri.getKey().get();
+    }
+    return new MFileDirectoryStream(new MFileS3Iterator(client, initialUri, prefix, limit, false));
+  }
+
   @Override
   public void close() {} // NO-OP
 
diff --git a/cdm/s3/src/main/java/thredds/inventory/s3/MFileS3.java b/cdm/s3/src/main/java/thredds/inventory/s3/MFileS3.java
index 8d9ab9bd08..1b5773b421 100644
--- a/cdm/s3/src/main/java/thredds/inventory/s3/MFileS3.java
+++ b/cdm/s3/src/main/java/thredds/inventory/s3/MFileS3.java
@@ -1,7 +1,8 @@
 /*
- * Copyright (c) 2020 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 2020-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
+
 package thredds.inventory.s3;
 
 import java.io.IOException;
@@ -218,9 +219,20 @@ public String getName() {
   @Nullable
   public MFile getParent() throws IOException {
     // In general, objects to do not have parents. However, if a delimiter is set, we have a pseudo path, and then
-    // the object can have a parent.
+    // the object can have a parent. If a delimiter is not set, but the key is not null, then the parent is
+    // the top of the bucket. If a delimiter is not set, and the key is null, then we are at the top of the bucket
+    // already, and then there is no parent.
     MFile parentMfile = null;
-    if (delimiter != null) {
+    if (delimiter == null) {
+      String key = getKey();
+      if (key != null && !key.isEmpty()) {
+        String uriString = getPath();
+        int queryIdx = uriString.indexOf("?");
+        if (queryIdx > 0) {
+          parentMfile = new MFileS3(uriString.substring(0, queryIdx));
+        }
+      }
+    } else {
       // get the full path
       String currentUri = getPath();
       String frag = "";
diff --git a/cdm/s3/src/test/java/thredds/inventory/s3/TestMFileS3.java b/cdm/s3/src/test/java/thredds/inventory/s3/TestMFileS3.java
index 6c7a2b1c07..676efa5490 100644
--- a/cdm/s3/src/test/java/thredds/inventory/s3/TestMFileS3.java
+++ b/cdm/s3/src/test/java/thredds/inventory/s3/TestMFileS3.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2020 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 2020-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -455,7 +455,8 @@ private void checkWithBucketAndKey(String cdmS3Uri, String expectedName, String
       if (delimiter != null) {
         assertThat(mFile.getParent()).isNotNull();
       } else {
-        assertThat(mFile.getParent()).isNull();
+        assertThat(mFile.getParent()).isNotNull();
+        assertThat(mFile.getParent().getPath()).isEqualTo(cdmS3Uri.split("\\?")[0]);
       }
       assertThat(mFile.isDirectory()).isFalse();
       assertThat(mFile.getLength()).isEqualTo(G16_OBJECT_1_SIZE);
@@ -468,8 +469,9 @@ private void dirCheckNoDelim(String cdmS3Uri, String expectedName) throws IOExce
       assertThat(mFile.getPath()).isEqualTo(cdmS3Uri);
       // Without a delimiter, the name is the key.
       assertThat(mFile.getName()).isEqualTo(expectedName);
-      // Without a delimiter, there is no parent.
-      assertThat(mFile.getParent()).isNull();
+      // Without a delimiter, the parent is the bucket.
+      assertThat(mFile.getParent()).isNotNull();
+      assertThat(mFile.getParent().getPath()).isEqualTo(cdmS3Uri.split("\\?")[0]);
       // Without a delimiter, there is no concept of a directory.
       assertThat(mFile.isDirectory()).isFalse();
     }
diff --git a/cdm/zarr/src/main/java/thredds/filesystem/zarr/ControllerZip.java b/cdm/zarr/src/main/java/thredds/filesystem/zarr/ControllerZip.java
index 365f87345c..0269645230 100644
--- a/cdm/zarr/src/main/java/thredds/filesystem/zarr/ControllerZip.java
+++ b/cdm/zarr/src/main/java/thredds/filesystem/zarr/ControllerZip.java
@@ -79,6 +79,21 @@ public DirectoryStream<MFile> getSubdirs(CollectionConfig mc, boolean recheck) {
     }
   }
 
+  @Override
+  public DirectoryStream<MFile> getFullInventoryAtLocation(String location) {
+    if (location.startsWith(prefix)) {
+      location = location.substring(prefix.length());
+    }
+
+    try {
+      MFileZip mfile = new MFileZip(location);
+      return new MFileDirectoryStream(new MFileIteratorLeaves(mfile));
+    } catch (IOException ioe) {
+      logger.warn(ioe.getMessage(), ioe);
+      return null;
+    }
+  }
+
   @Override
   public void close() {} // NOOP
 
diff --git a/grib/build.gradle.kts b/grib/build.gradle.kts
index 4e381669e3..a9a51d6e67 100644
--- a/grib/build.gradle.kts
+++ b/grib/build.gradle.kts
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2025 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 2025-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -39,6 +39,7 @@ dependencies {
 
   testCompileOnly(ncjLibs.junit4)
 
+  testRuntimeOnly(project(":cdm-s3"))
   testRuntimeOnly(project(":libaec-native"))
 
   testRuntimeOnly(ncjLibs.junit5.platformLauncher)
diff --git a/grib/src/main/java/ucar/nc2/grib/GribIndex.java b/grib/src/main/java/ucar/nc2/grib/GribIndex.java
index 4724e7b309..d5a51ed4b3 100644
--- a/grib/src/main/java/ucar/nc2/grib/GribIndex.java
+++ b/grib/src/main/java/ucar/nc2/grib/GribIndex.java
@@ -29,9 +29,7 @@ public abstract class GribIndex {
 
   private static final CollectionManager.ChangeChecker gribCC = new CollectionManager.ChangeChecker() {
     public boolean hasChangedSince(MFile file, long when) {
-      String idxPath = file.getPath();
-      if (!idxPath.endsWith(GBX9_IDX))
-        idxPath += GBX9_IDX;
+      String idxPath = makeIndexFileName(file.getPath());
       MFile idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
       if (idxFile == null)
         return true;
@@ -43,9 +41,7 @@ public boolean hasChangedSince(MFile file, long when) {
     }
 
     public boolean hasntChangedSince(MFile file, long when) {
-      String idxPath = file.getPath();
-      if (!idxPath.endsWith(GBX9_IDX))
-        idxPath += GBX9_IDX;
+      String idxPath = makeIndexFileName(file.getPath());
       MFile idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
       if (idxFile == null)
         return true;
@@ -91,14 +87,31 @@ public static GribIndex readOrCreateIndexFromSingleFile(boolean isGrib1, MFile m
     if (!index.readIndex(mfile.getPath(), mfile.getLastModified(), force)) { // heres where the index date is checked
                                                                              // against the data file
       index.makeIndex(mfile.getPath(), null);
-      logger.debug("  Index written: {} == {} records", mfile.getName() + GBX9_IDX, index.getNRecords());
+      logger.debug("  Index written: {} ({}) == {} records", mfile.getName(), GBX9_IDX, index.getNRecords());
     } else if (debug) {
-      logger.debug("  Index read: {} == {} records", mfile.getName() + GBX9_IDX, index.getNRecords());
+      logger.debug("  Index read: {} ({}) == {} records", mfile.getName(), GBX9_IDX, index.getNRecords());
     }
 
     return index;
   }
 
+  /**
+   * Make the gbx9 index name from the grib file name.
+   *
+   * Handles special cases where the grib filename is not a file path.
+   * For example
+   * cdms3:thredds-test-data?test-grib-without-index/cosmo-eu.grib2#delimiter=/
+   *
+   * becomes
+   * cdms3:thredds-test-data?test-grib-without-index/cosmo-eu.grib2.gbx9#delimiter=/
+   *
+   * @param filename
+   * @return the gbx9 index file
+   */
+  public static String makeIndexFileName(String filename) {
+    return GribUtils.makeIndexFileName(filename, GBX9_IDX);
+  }
+
   //////////////////////////////////////////
 
   /**
diff --git a/grib/src/main/java/ucar/nc2/grib/GribUtils.java b/grib/src/main/java/ucar/nc2/grib/GribUtils.java
index 5ac7059f29..c01e4fe21f 100755
--- a/grib/src/main/java/ucar/nc2/grib/GribUtils.java
+++ b/grib/src/main/java/ucar/nc2/grib/GribUtils.java
@@ -1,10 +1,12 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
 package ucar.nc2.grib;
 
+import thredds.inventory.MFile;
+import thredds.inventory.MFiles;
 import ucar.nc2.time.CalendarDate;
 import ucar.nc2.time.CalendarPeriod;
 import ucar.unidata.util.StringUtil2;
@@ -194,4 +196,28 @@ public static boolean scanModeSameDirection(int scanMode) {
     return !GribNumbers.testGribBitIsSet(scanMode, 4);
   }
 
+  /**
+   * Make an index filename with the given suffix from the grib filename.
+   *
+   * Handles special cases where the grib filename is not a file path.
+   * For example,
+   * cdms3:thredds-test-data?test-grib-without-index/cosmo-eu.grib2#delimiter=/
+   *
+   * becomes
+   * cdms3:thredds-test-data?test-grib-without-index/cosmo-eu.grib2.gbx9#delimiter=/
+   *
+   * @param filename
+   * @return the index filename
+   */
+  public static String makeIndexFileName(String filename, String idxNameSuffix) {
+    String idxPath = filename;
+    if (!filename.endsWith(idxNameSuffix)) {
+      MFile testIdxMFile = MFiles.create(filename);
+      String mfileName = testIdxMFile.getName();
+      String idxName = testIdxMFile.getName() + idxNameSuffix;
+      int i = idxPath.lastIndexOf(mfileName);
+      idxPath = idxPath.substring(0, i) + idxName + idxPath.substring(i + mfileName.length(), filename.length());
+    }
+    return idxPath;
+  }
 }
diff --git a/grib/src/main/java/ucar/nc2/grib/collection/GcMFile.java b/grib/src/main/java/ucar/nc2/grib/collection/GcMFile.java
index 733f5d8846..d379fdc959 100644
--- a/grib/src/main/java/ucar/nc2/grib/collection/GcMFile.java
+++ b/grib/src/main/java/ucar/nc2/grib/collection/GcMFile.java
@@ -33,7 +33,7 @@ static List<GcMFile> makeFiles(MFile directory, List<MFile> files, Set<Integer>
       MFile file = files.get(index);
       String filename;
       if (file.getPath().startsWith(dirPath)) {
-        filename = file.getPath().substring(dirPath.length());
+        filename = file.getName();
         if (filename.startsWith("/"))
           filename = filename.substring(1);
       } else
diff --git a/grib/src/main/java/ucar/nc2/grib/collection/GribCdmIndex.java b/grib/src/main/java/ucar/nc2/grib/collection/GribCdmIndex.java
index 9413c790c9..de1ed2176d 100644
--- a/grib/src/main/java/ucar/nc2/grib/collection/GribCdmIndex.java
+++ b/grib/src/main/java/ucar/nc2/grib/collection/GribCdmIndex.java
@@ -19,6 +19,7 @@
 import thredds.inventory.partition.*;
 import ucar.nc2.dataset.DatasetUrl;
 import ucar.nc2.grib.GribIndexCache;
+import ucar.nc2.grib.GribUtils;
 import ucar.nc2.grib.grib1.Grib1RecordScanner;
 import ucar.nc2.grib.grib2.Grib2RecordScanner;
 import ucar.nc2.stream.NcStream;
@@ -120,15 +121,25 @@ private static MFile makeTopIndexFileFromConfig(FeatureCollectionConfig config)
 
   static MFile makeIndexFile(String collectionName, MFile directory) {
     String nameNoBlanks = StringUtil2.replace(collectionName, ' ', "_");
-    return directory.getChild(nameNoBlanks + NCX_SUFFIX);
+    String indexFileName = GribUtils.makeIndexFileName(nameNoBlanks, NCX_SUFFIX);
+    return directory.getChild(indexFileName);
   }
 
-  private static String makeNameFromIndexFilename(String idxPathname) {
-    idxPathname = StringUtil2.replace(idxPathname, '\\', "/");
-    int pos = idxPathname.lastIndexOf('/');
-    String idxFilename = (pos < 0) ? idxPathname : idxPathname.substring(pos + 1);
-    assert idxFilename.endsWith(NCX_SUFFIX) : idxFilename;
-    return idxFilename.substring(0, idxFilename.length() - NCX_SUFFIX.length());
+  static String makeNameFromIndexFilename(String idxPathname) {
+    String name;
+    if (!idxPathname.endsWith(NCX_SUFFIX)) {
+      MFile testIdxMFile = MFiles.create(idxPathname);
+      String idxName = testIdxMFile.getName();
+      assert idxName.endsWith(NCX_SUFFIX) : idxName;
+      name = idxName.substring(0, idxName.length() - NCX_SUFFIX.length());
+    } else {
+      idxPathname = StringUtil2.replace(idxPathname, '\\', "/");
+      int pos = idxPathname.lastIndexOf('/');
+      String idxFilename = (pos < 0) ? idxPathname : idxPathname.substring(pos + 1);
+      assert idxFilename.endsWith(NCX_SUFFIX) : idxFilename;
+      name = idxFilename.substring(0, idxFilename.length() - NCX_SUFFIX.length());
+    }
+    return name;
   }
 
   ///////////////////////////////////////////
@@ -338,7 +349,7 @@ public static boolean updateGribCollection(FeatureCollectionConfig config, Colle
       if (specp.wantSubdirs()) { // its a partition
 
         try (DirectoryPartition dpart =
-            new DirectoryPartition(config, rootPath.toString(), true, new GribCdmIndex(logger), NCX_SUFFIX, logger)) {
+            new DirectoryPartition(config, rootPath, true, new GribCdmIndex(logger), NCX_SUFFIX, logger)) {
           dpart.putAuxInfo(FeatureCollectionConfig.AUX_CONFIG, config);
           changed = updateDirectoryCollectionRecurse(isGrib1, dpart, config, updateType, logger);
         }
@@ -834,9 +845,7 @@ private static GribCollectionImmutable openGribCollectionFromDataFile(boolean is
       throws IOException {
 
     String filename = dataRaf.getLocation();
-    File dataFile = new File(filename);
-
-    MFile mfile = new MFileOS(dataFile);
+    MFile mfile = MFiles.create(filename);
     return openGribCollectionFromDataFile(isGrib1, mfile, updateType, config, errlog, logger);
   }
 
diff --git a/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionImmutable.java b/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionImmutable.java
index 67f8f43269..792ed5d66a 100644
--- a/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionImmutable.java
+++ b/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionImmutable.java
@@ -1082,9 +1082,7 @@ public MFile findMFileByName(String filename) {
 
   RandomAccessFile getDataRaf(int fileno) throws IOException {
     // absolute location
-    MFile mfile = fileMap.get(fileno);
-    String filename = mfile.getPath();
-    MFile dataFile = MFiles.create(filename);
+    MFile dataFile = fileMap.get(fileno);
 
     // if data file does not exist, check relative location - eg may be /upc/share instead of Q:
     if (!dataFile.exists()) {
@@ -1103,7 +1101,7 @@ RandomAccessFile getDataRaf(int fileno) throws IOException {
       throw new FileNotFoundException("data file not found = " + dataFile.getPath());
     }
 
-    RandomAccessFile want = RandomAccessFile.acquire(dataFile.getPath());
+    RandomAccessFile want = NetcdfFiles.getRaf(dataFile.getPath(), -1);
     want.order(RandomAccessFile.BIG_ENDIAN);
     return want;
   }
diff --git a/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionMutable.java b/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionMutable.java
index fb542a319f..480e13be3e 100644
--- a/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionMutable.java
+++ b/grib/src/main/java/ucar/nc2/grib/collection/GribCollectionMutable.java
@@ -51,9 +51,9 @@ public class GribCollectionMutable implements Closeable {
   //////////////////////////////////////////////////////////
 
   static MFile makeIndexMFile(String collectionName, MFile directory) {
-    String nameNoBlanks = StringUtil2.replace(collectionName, ' ', "_");
-    return new GcMFile(directory, nameNoBlanks + GribCdmIndex.NCX_SUFFIX, -1, -1, -1); // LOOK dont know lastMod, size.
-                                                                                       // can it be added later?
+    MFile nameNoBlanks = GribCdmIndex.makeIndexFile(collectionName, directory);
+    return new GcMFile(directory, nameNoBlanks.getName(), -1, -1, -1); // LOOK dont know lastMod, size.
+                                                                       // can it be added later?
   }
 
   private static final CalendarDateFormatter cf =
diff --git a/grib/src/main/java/ucar/nc2/grib/grib1/Grib1Index.java b/grib/src/main/java/ucar/nc2/grib/grib1/Grib1Index.java
index 8614a7ae17..7ee69e5505 100644
--- a/grib/src/main/java/ucar/nc2/grib/grib1/Grib1Index.java
+++ b/grib/src/main/java/ucar/nc2/grib/grib1/Grib1Index.java
@@ -15,6 +15,7 @@
 import ucar.nc2.NetcdfFiles;
 import ucar.nc2.grib.GribIndex;
 import ucar.nc2.grib.GribIndexCache;
+import ucar.nc2.grib.GribUtils;
 import ucar.nc2.stream.NcStream;
 import ucar.unidata.io.RandomAccessFile;
 import java.io.File;
@@ -88,9 +89,7 @@ public boolean readIndex(String filename, long gribLastModified) {
   }
 
   public boolean readIndex(String filename, long gribLastModified, CollectionUpdateType force) {
-    String idxPath = filename;
-    if (!idxPath.endsWith(GBX9_IDX))
-      idxPath += GBX9_IDX;
+    String idxPath = GribIndex.makeIndexFileName(filename);
     MFile idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
     if (idxFile == null)
       return false;
@@ -169,11 +168,10 @@ private Grib1SectionGridDefinition readGds(Grib1IndexProto.Grib1GdsSection proto
 
   // LOOK what about extending an index ??
   public boolean makeIndex(String filename, RandomAccessFile dataRaf) throws IOException {
-    String idxPath = filename;
-    if (!idxPath.endsWith(GBX9_IDX))
-      idxPath += GBX9_IDX;
+    String idxPath = GribIndex.makeIndexFileName(filename);
     MFile idxMFile = GribIndexCache.getFileOrCache(idxPath);
-    MFile idxMFileTmp = GribIndexCache.getFileOrCache(idxPath + ".tmp");
+    String idxPathTmp = GribUtils.makeIndexFileName(idxPath, ".tmp");
+    MFile idxMFileTmp = GribIndexCache.getFileOrCache(idxPathTmp);
 
     if (!(idxMFile instanceof MFileOS || idxMFile instanceof MFileOS7)) {
       throw new IllegalArgumentException("Only local file systems are supported for index creation");
diff --git a/grib/src/main/java/ucar/nc2/grib/grib2/Grib2Index.java b/grib/src/main/java/ucar/nc2/grib/grib2/Grib2Index.java
index f2488f343f..da4f2a94bd 100644
--- a/grib/src/main/java/ucar/nc2/grib/grib2/Grib2Index.java
+++ b/grib/src/main/java/ucar/nc2/grib/grib2/Grib2Index.java
@@ -15,6 +15,7 @@
 import ucar.nc2.NetcdfFiles;
 import ucar.nc2.grib.GribIndex;
 import ucar.nc2.grib.GribIndexCache;
+import ucar.nc2.grib.GribUtils;
 import ucar.nc2.stream.NcStream;
 import ucar.unidata.io.RandomAccessFile;
 import java.io.File;
@@ -92,9 +93,7 @@ public boolean readIndex(String filename, long gribLastModified) {
   }
 
   public boolean readIndex(String filename, long gribLastModified, CollectionUpdateType force) {
-    String idxPath = filename;
-    if (!idxPath.endsWith(GBX9_IDX))
-      idxPath += GBX9_IDX;
+    String idxPath = GribIndex.makeIndexFileName(filename);
     MFile idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
     if (idxFile == null)
       return false;
@@ -204,11 +203,10 @@ private Grib2SectionGridDefinition readGds(Grib2IndexProto.GribGdsSection proto)
   // LOOK what about extending an index ??
   // Only support creation of index files locally
   public boolean makeIndex(String filename, RandomAccessFile dataRaf) throws IOException {
-    String idxPath = filename;
-    if (!idxPath.endsWith(GBX9_IDX))
-      idxPath += GBX9_IDX;
+    String idxPath = GribIndex.makeIndexFileName(filename);
     MFile idxMFile = GribIndexCache.getFileOrCache(idxPath);
-    MFile idxMFileTmp = GribIndexCache.getFileOrCache(idxPath + ".tmp");
+    String idxPathTmp = GribUtils.makeIndexFileName(idxPath, ".tmp");
+    MFile idxMFileTmp = GribIndexCache.getFileOrCache(idxPathTmp);
 
     if (!(idxMFile instanceof MFileOS || idxMFile instanceof MFileOS7)) {
       throw new IllegalArgumentException("Only local file systems are supported for index creation");
diff --git a/grib/src/test/java/ucar/nc2/grib/TestSingleGribFileS3.java b/grib/src/test/java/ucar/nc2/grib/TestSingleGribFileS3.java
new file mode 100644
index 0000000000..3598d884b1
--- /dev/null
+++ b/grib/src/test/java/ucar/nc2/grib/TestSingleGribFileS3.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright (c) 2026 University Corporation for Atmospheric Research/Unidata
+ * See LICENSE for license information.
+ */
+
+package ucar.nc2.grib;
+
+import static com.google.common.truth.Truth.assertThat;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.util.Formatter;
+import org.junit.Test;
+import ucar.ma2.Array;
+import ucar.nc2.Variable;
+import ucar.nc2.dataset.NetcdfDataset;
+import ucar.nc2.dataset.NetcdfDatasets;
+import ucar.nc2.util.CompareNetcdf2;
+import ucar.unidata.util.test.TestDir;
+
+public class TestSingleGribFileS3 {
+
+  private static final String GRIB1_BUCKET_KEY = "thredds-test-data?test-grib-without-index/radar_national.grib1";
+  private static final String GRIB2_BUCKET_KEY = "thredds-test-data?test-grib-without-index/cosmo-eu.grib2";
+  private static final String GRIB1_LOCAL = TestDir.localTestDataDir + "radar_national.grib1";
+  private static final String GRIB2_LOCAL = TestDir.localTestDataDir + "cosmo-eu.grib2";
+
+  @Test
+  public void testGrib1S3Full() throws IOException {
+    String location = String.format("cdms3://s3.us-east-1.amazonaws.com/%s#delimiter=/", GRIB1_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib1S3Short() throws IOException {
+    String location = String.format("cdms3:%s#delimiter=/", GRIB1_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib1SFullNoDelimiter() throws IOException {
+    String location = String.format("cdms3://s3.us-east-1.amazonaws.com/%s", GRIB1_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib1S3ShortNoDelimiter() throws IOException {
+    String location = String.format("cdms3:%s", GRIB1_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib2S3Full() throws IOException {
+    String location = String.format("cdms3://s3.us-east-1.amazonaws.com/%s#delimiter=/", GRIB2_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib2S3Short() throws IOException {
+    String location = String.format("cdms3:%s#delimiter=/", GRIB2_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib2SFullNoDelimiter() throws IOException {
+    String location = String.format("cdms3://s3.us-east-1.amazonaws.com/%s", GRIB2_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void testGrib2S3ShortNoDelimiter() throws IOException {
+    String location = String.format("cdms3:%s", GRIB2_BUCKET_KEY);
+    basicDatasetValidation(location);
+  }
+
+  @Test
+  public void compareGrib1() throws IOException {
+    String location = String.format("cdms3://s3.us-east-1.amazonaws.com/%s#delimiter=/", GRIB1_BUCKET_KEY);
+    compareWithLocal(location, GRIB1_LOCAL);
+  }
+
+  @Test
+  public void compareGrib2() throws IOException {
+    String location = String.format("cdms3://s3.us-east-1.amazonaws.com/%s#delimiter=/", GRIB2_BUCKET_KEY);
+    compareWithLocal(location, GRIB2_LOCAL);
+  }
+
+  private static void compareWithLocal(String remoteLocation, String localLocation) throws IOException {
+    try (NetcdfDataset remoteNetcdfDataset = NetcdfDatasets.openDataset(remoteLocation);
+        NetcdfDataset localNetcdfDataset = NetcdfDatasets.openDataset(localLocation)) {
+      Formatter f = new Formatter();
+      CompareNetcdf2 compare = new CompareNetcdf2(f, false, false, true);
+      if (!compare.compare(localNetcdfDataset, remoteNetcdfDataset, null)) {
+        System.out.printf("Compare %s%n%s%n", localLocation, f);
+        fail();
+      }
+    }
+  }
+
+  private static void basicDatasetValidation(String location) throws IOException {
+    try (NetcdfDataset netcdfDataset = NetcdfDatasets.openDataset(location)) {
+      assertThat(netcdfDataset.getLastModified()).isGreaterThan(0);
+      assertThat(netcdfDataset.getVariables()).isNotEmpty();
+
+      Variable variable = netcdfDataset.getVariables().get(1);
+      Array data = variable.read();
+      assertThat(data).isNotNull();
+    }
+  }
+}
diff --git a/grib/src/test/java/ucar/nc2/grib/collection/TestGribCdmIndex.java b/grib/src/test/java/ucar/nc2/grib/collection/TestGribCdmIndex.java
new file mode 100644
index 0000000000..e092f94dad
--- /dev/null
+++ b/grib/src/test/java/ucar/nc2/grib/collection/TestGribCdmIndex.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright (c) 2026 University Corporation for Atmospheric Research/Unidata
+ * See LICENSE for license information.
+ */
+
+package ucar.nc2.grib.collection;
+
+import static com.google.common.truth.Truth.assertThat;
+
+import org.junit.Test;
+import thredds.inventory.MFile;
+import thredds.inventory.MFiles;
+
+public class TestGribCdmIndex {
+
+  @Test
+  public void testMakeIndexFile() {
+    MFile directory = MFiles.create("/path/to/");
+    MFile idxMFile = GribCdmIndex.makeIndexFile("collection name", directory);
+    assertThat(idxMFile.getPath()).startsWith(directory.getPath());
+    assertThat(idxMFile.getName()).endsWith(GribCdmIndex.NCX_SUFFIX);
+
+
+    directory = MFiles.create("cdms3:bucket?path/to/#delimiter=/");
+    idxMFile = GribCdmIndex.makeIndexFile("collection name", directory);
+    assertThat(idxMFile.getPath()).startsWith("cdms3:bucket?path/to/");
+    assertThat(idxMFile.getPath()).endsWith("#delimiter=/");
+  }
+
+  @Test
+  public void testMakeNameFromIndexFilename() {
+    String indexFilename = "/path/to/collection_name" + GribCdmIndex.NCX_SUFFIX;
+    String expectedName = "collection_name";
+    String actualName = GribCdmIndex.makeNameFromIndexFilename(indexFilename);
+    assertThat(actualName).isEqualTo(expectedName);
+
+    indexFilename = "cdms3:bucket?path/to/collection_name" + GribCdmIndex.NCX_SUFFIX + "#delimiter=/";
+    actualName = GribCdmIndex.makeNameFromIndexFilename(indexFilename);
+    assertThat(actualName).isEqualTo(expectedName);
+  }
+
+}